My best guess is that you're running into the higher intermediate point (HIP) rule, but it would be hard to tell without digging a lot deeper. Even though stopovers are free in the fare rule, unless the HIP rule is waived in the fare rules then any time you add a stopover at, for example, point B in an A->B->C itinerary, the fare is repriced as the highest fare between A->B, B->C, and A->C. So while your original fare would have been SFO->TLV, it's possible that that the SFO->MUC or TLV->MUC fare might have been higher so you'd have to pay that fare once you added a stopover.
Re-faring the already-flown portion is pretty common in a situation like that. It would be nice to see the fare construction, but I don't think that United provides any way to see it for itineraries booked on united.com. It's entirely possible that the lowest priced option ended up being a SFO->MUC fare with a stopover in TLV or something similar.